library("tidyverse")
library("ggplot2")
library("sf")
library("dplyr")
library("lubridate")
library("ggbreak")
library("plotly")
library("ggrepel")
library("htmlwidgets")
library("directlabels")
library("rgdal")
library("httr")
library("geojsonsf")
library("leaflet")
library("leaflet.extras")
library("viridis")

Make custom palettes and theme

palette1= c("#FC4E2A","#BD0026")
palette2 = c("#045A8D","#3690C0")
palette3= c("#FC4E2A","#045A8D","#BD0026","#3690C0","#9970AB")
t3 <- list(family = 'Arial', size = 12)
theme_nyt <- function(){ 
    font <- "Arial"   #assign font family up front
    
    theme_bw() %+replace%    #replace elements we want to change
    
    theme(
      axis.title = element_text(             #axis titles
                   family = font,            #font family
                   size = 12),               #font size
      
      axis.text = element_text(              #axis text
                   family = font,            #axis famuly
                   size = 12),                #font size,
      
        #grid elements
        panel.border= element_blank())+theme(plot.background = element_rect("#FFFFFF"),
      
        legend.title = element_blank(),
        legend.text = element_text(family = font, size = 12),
        axis.title.x = element_blank(),
        axis.title.y = element_blank(),
        #legend.title=element_blank(),
        panel.background = element_rect(fill = "#FFFFFF"),
        panel.grid.major.x = element_blank(),
        panel.grid.major.y = element_line(linetype = "dashed"),
        panel.grid.minor.x = element_blank(),
        panel.grid.minor.y = element_blank(),
        axis.text.x = element_text(angle = 0,size=12, family=font, color = "black"),
        axis.text.y = element_text(family=font, face="plain", color="black", size=12, angle=0)) + theme(legend.position = "bottom")
}

#plotly theme

xaxis <- list(title = "",
             showline = FALSE,
             showgrid = FALSE)

yaxis <- list(title = "",
             showgrid = TRUE,
             zeroline = FALSE,
             showline = FALSE,
             showticklabels = TRUE)

Data Downloaded from https://raw.githubusercontent.com/nychealth/coronavirus-data/master/trends/data-by-day.csv. The data includes case number.

covid_nyc <- read.csv("./COVID-19_Daily_Counts_of_Cases__Hospitalizations__and_Deaths.csv", stringsAsFactors = F)

covid_nyc <- covid_nyc %>% mutate(date_of_interest = mdy(date_of_interest))

Deaths due to Covid-19 in New York since February 2020

full_join (covid_nyc %>% dplyr::select(date_of_interest, DEATH_COUNT) %>%
    mutate(type = "Confirmed Covid-19 Death"),
  covid_nyc %>% dplyr::select(date_of_interest, DEATH_COUNT = PROBABLE_DEATH_COUNT) %>%
    mutate(type = "Assumed Covid-19 Death")) %>% 
  ggplot(aes(x = date_of_interest, y = DEATH_COUNT, color = type)) + 
  stat_smooth(method = 'loess',n = 500, span=1/60, se = FALSE) + 
  scale_color_manual(values= palette1, guide = guide_legend(override.aes = list(shape = c(16, 18))))  + 
   ggtitle("Covid-19 Deaths \n New York City")+
  theme_nyt()+ theme(plot.title = element_text(size=17))

# ggsave("Covid_19_new_york_2020_2023.png", width = 6, height = 4, dpi = 300)

plotly version

plotly_df_death <- full_join (covid_nyc %>% dplyr::select(date_of_interest, DEATH_COUNT)%>%
    mutate(type = "Confirmed Covid-19 Death"), 
    covid_nyc %>% dplyr::select(date_of_interest, DEATH_COUNT = PROBABLE_DEATH_COUNT) %>%
  mutate(type = "Assumed Covid-19 Death"))


plot_ly(x = ~plotly_df_death$date_of_interest, y = ~plotly_df_death$DEATH_COUNT, color = plotly_df_death$type, type = "scatter", mode = "lines", colors = c("#FC4E2A","#BD0026"), line = list(shape = 'line', smoothing = 1), width = 4) %>%
  layout(title = list(text = paste0('Covid-19 Deaths',
                                    '<br>',
                                    '<sup>',
                                    'New York City',
                                    '</sup>')), 
         legend = list(orientation = "h",   # show entries horizontally
                     xanchor = "center",  # use center of legend as anchor
                     x = 0.5),           # put legend in center of x-axis
         font = list(family = "Arial", size = 17), xaxis = xaxis, yaxis = yaxis, margin = list(t = 80))
Jul 2020Jan 2021Jul 2021Jan 2022Jul 2022Jan 20230100200300400500600
Assumed Covid-19 DeathConfirmed Covid-19 DeathCovid-19 Deaths​New York City​

Covid-19 cases in New York City since February 2020

full_join (covid_nyc %>% dplyr::select(date_of_interest, CASE_COUNT)%>%
             mutate(type = "Confirmed Covid-19 Patient"),covid_nyc %>% 
             dplyr::select(date_of_interest, CASE_COUNT = PROBABLE_CASE_COUNT) %>%
             mutate(type = "Assumed Covid-19 Patient")) %>%
  ggplot(aes(x = date_of_interest, y = CASE_COUNT, color = type)) + 
  stat_smooth(method = 'loess',n = 500, span=1/60, se = FALSE) + 
  scale_color_manual(values= palette2, guide = guide_legend(override.aes = list(shape = c(16, 18))))  + 
  scale_y_continuous(expand = c(0,0)) + 
   ggtitle("Covid-19 Reported Cases \n New York City")+
  theme_nyt()+ theme(plot.title = element_text(size=17))

#ggsave("Covid_19_new_york_2020_2023_cases.png", width = 6, height = 4, dpi = 300)

plotly verrsion

plotly_df_patient <- full_join (covid_nyc %>% dplyr::select(date_of_interest, CASE_COUNT)%>%
             mutate(type = "Confirmed Covid-19 Patient"),covid_nyc %>% 
             dplyr::select(date_of_interest, CASE_COUNT = PROBABLE_CASE_COUNT) %>%
             mutate(type = "Assumed Covid-19 Patient")) 

plot_ly(x = ~plotly_df_patient$date_of_interest, y = ~plotly_df_patient$CASE_COUNT, color = plotly_df_patient$type, type = "scatter", mode = "lines", colors = c("#045A8D","#3690C0"), line = list(shape = 'line', smoothing = 1), width = 4) %>%
  layout(title = list(text = paste0('Covid-19 Reported Cases',
                                    '<br>',
                                    '<sup>',
                                    'New York City',
                                    '</sup>')), 
         legend = list(orientation = "h",   # show entries horizontally
                     xanchor = "center",  # use center of legend as anchor
                     x = 0.5),           # put legend in center of x-axis
         font = list(family = "Arial", size = 17), xaxis = xaxis, yaxis = yaxis, margin = list(t = 80))
Jul 2020Jan 2021Jul 2021Jan 2022Jul 2022Jan 2023010k20k30k40k50k
Assumed Covid-19 PatientConfirmed Covid-19 PatientCovid-19 Reported Cases​New York City​
covid_nyc %>% dplyr::select(date_of_interest, HOSPITALIZED_COUNT) %>% 
  ggplot(aes(x = date_of_interest, y = HOSPITALIZED_COUNT)) + 
  stat_smooth(method = 'loess',n = 500, span=1/60, se = FALSE, color = "#9970AB")  + 
  scale_y_continuous(expand = c(0,0)) + 
  labs(title = "Covid-19 Hospitalizations", subtitle = "New York City") + 
  theme_nyt() 

#ggsave("./final_figures/hospitalizations_covid_19_new_york_2020_2023.png", width = 6, height = 4, dpi = 300)
plotly_df <- covid_nyc %>% dplyr::select(date_of_interest, HOSPITALIZED_COUNT) 
plot_ly(x = ~plotly_df$date_of_interest, y = ~plotly_df$HOSPITALIZED_COUNT, type = "scatter", mode = "lines", line = list(shape = 'line', smoothing = 1, color = "#6B5B95",width = 4)) %>%
  layout(title = list(text = paste0('Covid-19 Hospitalizations',
                                    '<br>',
                                    '<sup>',
                                    'New York City',
                                    '</sup>')), 
         font = list(family = "Arial", size = 17), xaxis = xaxis, yaxis = yaxis, margin = list(t = 80))
Jul 2020Jan 2021Jul 2021Jan 2022Jul 2022Jan 2023050010001500
Covid-19 Hospitalizations​New York City​
df = rbind((full_join(covid_nyc %>% dplyr::select(date_of_interest, CASE_COUNT)%>%
             mutate(label = "Confirmed Patient"),covid_nyc %>% 
             dplyr::select(date_of_interest, CASE_COUNT = PROBABLE_CASE_COUNT) %>%
             mutate(label = "Assumed Patient")) %>% 
              mutate(count = CASE_COUNT) %>% 
              dplyr::select(date_of_interest, count, label)),
full_join(covid_nyc %>% dplyr::select(date_of_interest, DEATH_COUNT) %>%
             mutate(label = "Confirmed Death"),covid_nyc %>% 
             dplyr::select(date_of_interest, DEATH_COUNT = PROBABLE_DEATH_COUNT) %>%
            mutate(label = "Assumed Death"))%>% mutate(count =DEATH_COUNT) %>% 
            dplyr::select(date_of_interest, count, label)) %>% 
            rbind(covid_nyc %>% dplyr::select(date_of_interest, HOSPITALIZED_COUNT) %>% 
            mutate(count = HOSPITALIZED_COUNT, label = "Hospitalized") %>% 
            dplyr::select(date_of_interest, count, label)) 
 # last <- max(df$date_of_interest)
ggplot(data = df, aes(x = (date_of_interest), y = count, color = label, label = label)) + 
  stat_smooth(method = 'loess',n = 500, span=1/60, se = FALSE)+ 
  scale_color_manual(values= palette3) +
  scale_y_sqrt(breaks = c(0,800, 1600, 2400, 4800,10000, 20000, 30000, 40000),
               labels = c("0","800", "1600","2400", "4800","10000", "20000", "30000", "40000")) +
  labs(title = "Covid-19 Cases", subtitle = "New York City") +
  theme_nyt()+theme(legend.position = "none")

#ggsave("./final_figures/all_new_york_2020_2023.png",bg = FALSE,  dpi = 300)
CovidDat <- read.csv('https://raw.githubusercontent.com/nychealth/coronavirus-data/master/totals/data-by-modzcta.csv', stringsAsFactors = F)
  Neighborhoods  <- geojson_sf("./nychealth_coronavirus_data master_Geography_resources/MODZCTA_2010_WGS1984.geo.json")


CovidDat <- CovidDat %>% mutate(DEATH_RATE = (COVID_DEATH_COUNT/COVID_CASE_COUNT)*100) 

infern <- inferno(n = 7, direction = -1)
inner_join(Neighborhoods, CovidDat, by = 'label') -> MapData 
pal_death_rate <- colorBin(infern, MapData$DEATH_RATE, #or colorNumber 
                                   na.color = "pink") 

leaflet() %>% 
  addPolygons(data = MapData,
              label = ~NEIGHBORHOOD_NAME,
              weight = 1.2,
              fillColor = ~pal_death_rate(DEATH_RATE),
              fillOpacity = 1,
              color = "black") %>%
  addLegend(data = MapData,
           pal = pal_death_rate,
            values = ~DEATH_RATE,
            opacity = 1,
            title="Covid-19 Death Rate") %>%
  setMapWidgetStyle(style = list(background = "white"))
+−
Covid-19 Death Rate
0.0 – 0.5
0.5 – 1.0
1.0 – 1.5
1.5 – 2.0
2.0 – 2.5
2.5 – 3.0
3.0 – 3.5
Leaflet